- Introduction to single-cell RNA-seq
- Quality control and normalization
- Survey of downstream analysis methodology
July 6, 2019
Amezquita et al. 2019 (https://doi.org/10.1101/590562)
## class: SingleCellExperiment ## dim: 23918 192 ## metadata(0): ## assays(1): counts ## rownames(23918): ENSMUSG00000103377 ENSMUSG00000103147 ... ## ERCC-00171 CBFB-MYH11-mcherry ## rowData names(13): GeneLength ENSEMBL ... total_counts ## log10_total_counts ## colnames(192): SLX-9555.N701_S502.C89V9ANXX.s_1.r_1 ## SLX-9555.N701_S503.C89V9ANXX.s_1.r_1 ... ## SLX-11312.N712_S508.H5H5YBBXX.s_8.r_1 ## SLX-11312.N712_S517.H5H5YBBXX.s_8.r_1 ## colData names(48): Plate Oncogene ... ## pct_counts_in_top_500_features_ERCC PlateOnco ## reducedDimNames(0): ## spikeNames(1): ERCC
This SingleCellExperiment object has 23918 genes and 192 cells.
Lun et al. 2019, (https://doi.org/10.1186/s13059-019-1662-y)
Lun et al. 2019, (https://doi.org/10.1186/s13059-019-1662-y)
scran: Lun et al. 2016 (https://doi.org/10.1186/s13059-016-0947-7) proposed a pooling & deconvolution approach
Cells are pooled together and normalized against a global pseudoreference, then deconvolved by solving a system of linear equations
Bacher et al. 2017 (https://doi.org/10.1038/nmeth.4263)
Hafemeister & Satija 2019 (https://doi.org/10.1101/576827)
When batches are known and cell populations are identical across batches \(z_b\) (e.g. evenly split across two plates & homogeneous), can estimate effects due to batch
see also Combat: Johnson & Rabinovic 2007 (https://doi.org/10.1093/biostatistics/kxj037), implemented in sva
- MNNcorrect: Haghverdi et al. 2018 (https://doi.org/10.1038/nbt.4091) aligns cells based on their mutual nearest neigbors
Haghverdi et al. 2018 (https://doi.org/10.1038/nbt.4091)
Andrews & Hemburg 2019 (https://doi.org/10.12688/f1000research.16613.1)